A bioassay is a procedure where a property, concentration or presence of a biological analyte is measured in a sample. Bioassays are an intrinsic part of research in all fields of science, most notably in life sciences and especially in molecular biology.
A particular type of analysis in molecular biology relates to genotyping and sequencing. Genotyping and sequencing refers to the process of determining the genotype of an individual with a biological assay. Current methods include PCR, DNA and RNA sequencing, and hybridization to DNA and RNA microarrays mounted on various carriers such as glass plates or beads. The technology is intrinsic for test on father/motherhood, in clinical research for the investigation of disease-associated genes and in other research aimed at investigating the genetic control of properties of any species for instance whole genome scans for QTL's (Quantitative Trait Loci).
Due to current technological limitations, almost all genotyping is partial. That is, only a small fraction of an individual's genotype is determined. In many instances this is not a problem. For instance, when testing for father-/motherhood, only 10 to 20 genomic regions are investigated to determine relationship or lack thereof, which is a tiny fraction of the human genome.
Single nucleotide polymorphisms (SNPs) are the most abundant type of polymorphism in the genome. With the parallel developments of dense SNP marker maps and technologies for high-throughput SNP genotyping, SNPs have become the markers of choice for many genetic studies. A substantial number of samples is required in mapping and association studies or in genomic selection experiments.
In order to provide for high-throughput genotyping capabilities, arraying technologies have been developed. Such technologies are available from commercial suppliers such as Affymetrix (microarray-based GeneChip® Mapping arrays), Illumina (BeadArray™), Biotrove (Open Array™) and Sequenom (MassARRAY™). In many species (humans, livestock, plants, bacteria and viruses) a large number of SNPs is available or will become available in the near future. New innovations have enabled whole-genome genotyping or association studies and associated whole-genome selection programs for plant and animal breeding. Yet the costs of such programs are still significant, requiring budgets of up to several millions of dollars if samples are individually genotyped. Therefore, studies aimed at identifying SNPs in any species, currently involve analysis of only a limited number of individuals. The current invention therefore is of great significance since it allows a very substantial reduction of the cost of genotyping.
In order to obtain full insight in genomic variability it is necessary to know the full sequence of (a relevant part of) the genome. However, the cost of determining the full sequence is even higher than the cost of genotyping which is described in the previous paragraph. Despite the costs, it is expected that sequencing will replace genotyping to provide individual genotypes for the entire genome or specific regions thereof. The current invention also provides methods to reduce the cost of sequencing.
Sample pooling is regularly used in studies on categorical traits as a means to reduce analysis costs. The presence of the characteristic in the pool, consisting of a mixture of several samples indicates the presence of that characteristic in at least one of the samples in that pool. DNA pools are for instance used for:                estimating allele frequencies in a population.        By taking a good sample of individuals from the population, the raw allele frequency of allele 1 is calculated as the ratio between the result for allele 1 and the sum of the result for allele1 and the result for allele2 in the pool.        case-control association studies wherein cases and controls are divided into separate pools, and        reconstructing haplotypes on a limited number of individuals and a limited number of SNPs.        Based on the allele frequencies measured in the pool, haplotypes can be estimated by different algorithms such as maximum likelihood. The term haplotype frequency is synonymous with the term joint distribution of markers.        
An important disadvantage of sample pooling is that the measured characteristic is only identified in the pool as a whole, and not in any of the individual samples in the pool. One exception is DNA pools for genotyping trios (father, mother and child) when two pools each consisting of two individuals are created (father+child and mother+child). The observed allele frequency in each pool is indicative of the genotypes for all 3 individuals. This type of sample pooling provides a cost reduction of 33% but is only possible with such trios. In all other instances, pooled samples must be re-analysed individually in order to provide results for the individual samples.
Thus, it would be beneficial to provide sample pools for sample types other than trios, while still providing test results for the individual samples within that pool.